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Structure of Trypanosoma cruzi dihydroorotate dehydrogenase in complex with MII-5-170
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3W70 PDB ENTRY 3W70
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.2 277 0.1M Cacodylate, 13% PEG3350, 0.05M Hexaamminecobalt (III) Chloride, 1mM Oxonate, pH 5.2, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.31 46.74
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.994 α = 90 b = 71.567 β = 90 c = 129.346 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 77 CCD ADSC QUANTUM 270 2009-11-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-17A 0.98 Photon Factory BL-17A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 1.52 50 99.2 0.065 10 5.5 96556 -3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.52 1.55 100 0.433 3.18 5.4 4752
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 3W70 1.52 49.34 96480 4820 99.1 0.1464 0.145 0.1661 0.1735 0.1906 RANDOM 15.7625
Temperature Factor Modeling Anisotropic B[1][1] Anisotropic B[1][2] Anisotropic B[1][3] Anisotropic B[2][2] Anisotropic B[2][3] Anisotropic B[3][3] -0.1 -0.19 0.29
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.701 r_dihedral_angle_4_deg 19.455 r_dihedral_angle_3_deg 11.981 r_dihedral_angle_1_deg 6.925 r_angle_refined_deg 2.503 r_mcangle_it 2.294 r_mcbond_it 1.608 r_mcbond_other 1.607 r_angle_other_deg 1.265 r_chiral_restr 0.212
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.701 r_dihedral_angle_4_deg 19.455 r_dihedral_angle_3_deg 11.981 r_dihedral_angle_1_deg 6.925 r_angle_refined_deg 2.503 r_mcangle_it 2.294 r_mcbond_it 1.608 r_mcbond_other 1.607 r_angle_other_deg 1.265 r_chiral_restr 0.212 r_bond_refined_d 0.026 r_gen_planes_refined 0.016 r_bond_other_d 0.003 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4776 Nucleic Acid Atoms Solvent Atoms 674 Heterogen Atoms 215
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data collection